[gmx-users] energy minimization
dallas.warren at monash.edu
Tue Sep 25 23:16:05 CEST 2018
Look around atom 2016, there is a bad contact between the atoms in that
area, hence the infinite force, very high potential energy, and the
On Tue, 25 Sep. 2018, 6:48 pm ikjk, <1761440083 at qq.com> wrote:
> I am doing a md with martini force filed,I create a box, there is a
> double monolayer, then I solvate it, but when I did energy minimization,
> gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr then
> NOTE 1 [file minim.mdp]:
> With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> that with the Verlet scheme, nstlist has no effect on the accuracy of
> your simulation.
> Setting the LD random seed to 562058480
> Generated 0 of the 780 non-bonded parameter combinations
> Excluding 1 bonded neighbours molecule type 'DPPC'
> Excluding 1 bonded neighbours molecule type 'W'
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are: 72143 Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 261042.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 168x168x208, spacing 0.118 0.118 0.118
> Estimate for the relative computational
> load of the PME mesh part: 0.91
> NOTE 2 [file minim.mdp]:
> The optimal PME mesh load for parallel simulations is below 0.5
> and for highly parallel simulations between 0.25 and 0.33,
> for higher performance, increase the cut-off and the PME grid spacing.
> gmx mdrun -v -deffnm em
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e+03
> Number of steps = 50000
> Step= 14, Dmax= 1.2e-06 nm, Epot= 2.36880e+22 Fmax= inf, atom=
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your
> It stopped because the algorithm tried to make a new step whose size was
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> writing lowest energy coordinates.
> it just stopped with 14 steps, here is my mdp file,if you can solve this
> problem, I will appreciate that.
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent
> emtol = 1000.0 ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> emstep = 0.01 ; Minimization step size
> nsteps = 50000 ; Maximum number of (minimization) steps to
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor list and
> long range forces
> cutoff-scheme = Verlet ; Buffered neighbor searching
> ns_type = grid ; Method to determine neighbor list (simple,
> coulombtype = PME ; Treatment of long range electrostatic
> rcoulomb = 1.0 ; Short-range electrostatic cut-off
> rvdw = 1.0 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions in all 3
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users